Dataset of protein species from human liver

Naryzhny, Stanislav N.; Maynskova, Maria A.; Zgoda, Victor G.; Archakov, Alexander I.

doi:10.1016/j.dib.2017.04.051

Cited by 7 publications

(10 citation statements)

References 14 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…WB was performed as described [13] with primary antibodies against FN (ab2413; Abcam, USA) and CD63 (ab68418; Abcam, USA) followed by a peroxidase-labeled secondary antibody (A0545; Sigma, Germany). MS (shotgun analysis) of exosomal proteins was performed according to the filteraided sample preparation (FASP) protocol [16,17]. Briefly, the proteins were digested with trypsin (Promega Trypsin Gold), and MS/MS analysis of resulting peptides was performed in duplicate using an Orbitrap Fusion Lumos MS (Thermo Scientific, USA) [18,19].The data were searched by Mascot 2.4.1 (http://www.matrixscience.com/).…”

Section: Enzymatic Modification and Analysis Of Plasma Exosomesmentioning

confidence: 99%

Functional Properties of Circulating Exosomes Mediated by Surface-Attached Plasma Proteins

Shtam¹,

Naryzhny²,

Kopylov³

et al. 2018

J Hematol

Self Cite

View full text Add to dashboard Cite

Background: Exosomes and other types of extracellular vesicles present an important component of circulating plasma. Exosomes released by endothelial and blood cells account for majority of plasma exosomal population; exosomes secreted by other cells might cross tissue-plasma barrier and reach circulating plasma as well. Definitely, exosomes of different cellular origins are different by content and function. However, exosomal surface membrane interacts with plasma components. This interaction may alter composition of exosomal surface and hence, provide these vesicles with new functional properties. This study was aimed to estimate composition and possible functional role of proteins attached on the surface of plasma exosomes. Methods: Here, extracellular vesicles from human plasma were isolated by ultracentrifugation and treated by trypsin. Trypsinized and native exosomes were analyzed by nanoparticle tracking analysis, Western blotting and quantitative high-resolution mass spectrometry. Results: Surface-attached proteins were removed from exosomes isolated from plasma of healthy donors by incubation with serine protease (trypsin). Treatment did not impact exosomes integrity while slightly reduced hydrodynamic radius. Mass spectrometry revealed 259 exosomal proteins; among them 79 proteins were completely removed and more than half of the proteins were partially removed by trypsinization. Gene ontology functional annotation revealed mostly extracellular locations of proteins cleaved from a surface of the plasma exosomes. Moreover, proteins cleaved from the exosome surface are supposed to be implicated into integrin-linked kinase (ILK), focal adhesion kinase (FAK) and other pathways connecting cell surface with intracellular signaling cascades. Conclusion: Taken together, our results demonstrate that a surface of circulating exosomes is decorated by plasma proteins, and these proteins can mask tissue-specific characteristic of the exosomal surface membrane and provide exosomes with new and uniform properties.

show abstract

Section: Enzymatic Modification and Analysis Of Plasma Exosomesmentioning

confidence: 99%

Functional Properties of Circulating Exosomes Mediated by Surface-Attached Plasma Proteins

Shtam¹,

Naryzhny²,

Kopylov³

et al. 2018

J Hematol

Self Cite

View full text Add to dashboard Cite

show abstract

“…We have performed a panoramic study of human proteins and their proteoforms using a cancer cell line (HepG2) and normal liver tissue. Previously, some of these data were already published [ 7 , 19 ]. We generated the list of proteins identified in liver and HepG2 cell extracts using treatment with trypsin according to the FASP protocol [ 23 ], and by separation according to pI/Mw using 2DE, followed by sectional analysis of the gel by ESI LC-MS/MS.…”

Section: Resultsmentioning

confidence: 99%

“…We generated the list of proteins identified in liver and HepG2 cell extracts using treatment with trypsin according to the FASP protocol [ 23 ], and by separation according to pI/Mw using 2DE, followed by sectional analysis of the gel by ESI LC-MS/MS. A total of 20,462 proteoforms encoded by 3773 genes were identified in the case of HepG2 cells [ 7 ], and 14,667 proteoforms, encoded by 3305 genes, in the case of liver cells [ 19 ]. Here, we present further analyses of these data.…”

Section: Resultsmentioning

confidence: 99%

“…Liver tissue samples were provided within the framework of collaboration with the Chromosome-Centric Human Proteome Project (C-HPP). Extraction was performed by lysis after grinding the tissue in liquid nitrogen according to two-dimensional electrophoresis (2DE) protocol described in [ 19 ]. All procedures for 2DE were carried out as described previously [ 7 , 20 , 21 ].…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Variety and Dynamics of Proteoforms in the Human Proteome: Aspects of Markers for Hepatocellular Carcinoma

et al. 2017

Self Cite

View full text Add to dashboard Cite

We have previously developed an approach, where two-dimensional gel electrophoresis (2DE) was used, followed by sectional analysis of the whole gel using high-resolution nano-liquid chromatography-mass spectrometry (ESI LC-MS/MS). In this study, we applied this approach on the panoramic analysis of proteins and their proteoforms from normal (liver) and cancer (HepG2) cells. This allowed us to detect, in a single proteome, about 20,000 proteoforms coded by more than 4000 genes. A set of 3D-graphs showing distribution of these proteoforms in 2DE maps (profiles) was generated. A comparative analysis of these profiles between normal and cancer cells showed high variability and dynamics of many proteins. Among these proteins, there are some well-known features like alpha-fetoprotein (FETA) or glypican-3 (GPC3) and potential hepatocellular carcinoma (HCC) markers. More detailed information about their proteoforms could be used for generation of panels of more specific biomarkers.

show abstract

“…), or a rare type of biomaterial (umbilical cord blood, placenta, aborted material, etc.). Part of the data was previously published [49][50][51][52][53][54][55][56], and some of them were internal proteomic profiling experiments. In total, 25 types of biomaterials were analyzed, where seven proteins were detected by two peptides (one of which is unique) with varying degrees of reliability-two missing and five uncertain ( Table 2, Supplementary note 1, Supplementary Table S2).…”

Section: Unique Cases-beyond the C-hpp Scopementioning

confidence: 99%

Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins

et al. 2020

Self Cite

View full text Add to dashboard Cite

Despite direct or indirect efforts of the proteomic community, the fraction of blind spots on the protein map is still significant. Almost 11% of human genes encode missing proteins; the existence of which proteins is still in doubt. Apparently, proteomics has reached a stage when more attention and curiosity need to be exerted in the identification of every novel protein in order to expand the unusual types of biomaterials and/or conditions. It seems that we have exhausted the current conventional approaches to the discovery of missing proteins and may need to investigate alternatives. Here, we present an approach to deciphering missing proteins based on the use of non-standard methodological solutions and encompassing diverse MS/MS data, obtained for rare types of biological samples by members of the Russian Proteomic community in the last five years. These data were re-analyzed in a uniform manner by three search engines, which are part of the SearchGUI package. The study resulted in the identification of two missing and five uncertain proteins detected with two peptides. Moreover, 149 proteins were detected with a single proteotypic peptide. Finally, we analyzed the gene expression levels to suggest feasible targets for further validation of missing and uncertain protein observations, which will fully meet the requirements of the international consortium. The MS data are available on the ProteomeXchange platform (PXD014300).

show abstract

Dataset of protein species from human liver

Cited by 7 publications

References 14 publications

Functional Properties of Circulating Exosomes Mediated by Surface-Attached Plasma Proteins

Functional Properties of Circulating Exosomes Mediated by Surface-Attached Plasma Proteins

Variety and Dynamics of Proteoforms in the Human Proteome: Aspects of Markers for Hepatocellular Carcinoma

Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins

Contact Info

Product

Resources

About